Gold standard procedure in Auto3DEM

[Giovanni Cardone]

Dear users,

starting with the new version 4.05 of Auto3DEM, it is possible to follow
what has been recently defined as 'gold standard procedure' (called
'unbiased model reconstruction method' in the original paper on Auto3DEM
by Yan et. al, 2007) in a way that is almost transparent to the user.
The procedure consists of splitting the data into two half sets of
particles, at the beginning of the iterative procedure: at each
iteration each set generates an independent reconstruction, which is
used as a reference, against the same set, for the next cycle of origin
and orientation refinement.
In the parameter file controlling the workflow of Auto3DEM (usually
ending with _master or _continue) there is a new flag in the control
parameters, that is 'auto gold_standard', which is set to 1 by default.
Also, the reference maps for the two independent sets are specified in
the fields 'auto start_map_even' and 'auto start_map_odd'. In order to
succesfully run the procedure, an additional constraint is required: the
input stack parameter files need to be already organized into two
independent sets. This is automatically obtained when using the random
model computation procedure to generate an ab-initio reference map,
otherwise the two stacks can be generated by using the general purpose
program autopp (option 6). Since the approach used to generate two
independent sets of particles is to split them according to their
sequential numbering in each stack (even-numbered particles are assigned
to one set and odd-numbered to the other), the convention adopted is
that the extension of the stack parameter files reflects the set their
particles belong:
.dat_XXX -> all particles from the stack
.date_XXX -> only even-numbered particles from the stack
.dato_XXX -> only odd-numbered particles from the stack
where XXX is the iteration number the parameters refer to.
It is to remark that the strategy to split the data into two independent
sets can actually be arbitrary, as long as the parameter files follow
this convention. However, for different strategies the user needs to
generate the .date and .dato files on his/her own, since autopp only
splits by sequential numbering.
As a result of the procedure, after each iteration three maps are
actually generated: one from each set and one from all the particles.
The last one is just for visualization purposes, and only its radial
amplitude profile is utilized to re-calibrate some masking parameters.
Currently the implementation has one caveat: in case the two
reconstructions converge to maps with opposite handedness, the program
is not able to detect it, and therefore it will not be able to improve
the reconstruction beyond the resolution where the handedness becomes
evident. We are working to eliminate this inconvenience, and the moment
the simplest solution is to compare visually the two independent maps,
and if the handedness is different then:
1. modify the stack parameter files from the last iteration, for only
one set, using the command handflip;
2. change the handedness of the corresponding reconstruction. This can
be done either recomputing the reconstruction from the modified
parameter files (in the last _continue file, just set 'auto
generate_map' to 'only' and launch it), or by modifying the map using an
external program (e.g. using the program bimg from bsoft, with the
option '-reslice xy-z').

Sincerely,
Giovanni